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Jörg Hakenberg
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2010 – 2019
- 2016
- [j16]Wei-Yi Cheng, Jörg Hakenberg
, Shuyu Dan Li, Rong Chen:
DIVAS: a centralized genetic variant repository representing 150 000 individuals from multiple disease cohorts. Bioinform. 32(1): 151-153 (2016) - [j15]Benjamin S. Glicksberg
, Li Li
, Marcus A. Badgeley
, Khader Shameer, Roman Kosoy, Noam D. Beckmann, Nam Pho, Jörg Hakenberg, Meng Ma, Kristin L. Ayers
, Gabriel E. Hoffman, Shuyu Dan Li, Eric E. Schadt, Chirag J. Patel, Rong Chen, Joel T. Dudley:
Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks. Bioinform. 32(12): 101-110 (2016) - [j14]Philippe Thomas, Tim Rocktäschel, Jörg Hakenberg, Yvonne Lichtblau, Ulf Leser:
SETH detects and normalizes genetic variants in text. Bioinform. 32(18): 2883-2885 (2016) - [j13]Jörg Hakenberg
, Wei-Yi Cheng, Philippe Thomas, Ying-Chih Wang, Andrew V. Uzilov, Rong Chen:
Integrating 400 million variants from 80, 000 human samples with extensive annotations: towards a knowledge base to analyze disease cohorts. BMC Bioinform. 17: 24 (2016) - 2015
- [c13]Benjamin S. Glicksberg, Li Li, Wei-Yi Cheng, Khader Shameer, Jörg Hakenberg, Rafael Castellanos, Meng Ma, Lisong Shi, Hardik Shah, Joel T. Dudley, Rong Chen:
An Integrative Pipeline for Multi-Modal Discovery of Disease Relationships. Pacific Symposium on Biocomputing 2015: 407-418 - 2013
- [j12]Jörg Hakenberg
, Goran Nenadic
, Dietrich Rebholz-Schuhmann, Jin-Dong Kim:
Literature Mining Solutions for Life Science Research. Adv. Bioinformatics 2013: 320436:1-320436:2 (2013) - 2012
- [j11]Jörg Hakenberg
, Dmitry Voronov, Nguyen Ha Vo, Shanshan Liang, Saadat Anwar, Barry Lumpkin, Robert Leaman, Luis Tari, Chitta Baral:
A SNPshot of PubMed to associate genetic variants with drugs, diseases, and adverse reactions. J. Biomed. Informatics 45(5): 842-850 (2012) - [j10]Luis Tari, Phan Huy Tu, Jörg Hakenberg
, Yi Chen
, Tran Cao Son, Graciela Gonzalez
, Chitta Baral:
Incremental Information Extraction Using Relational Databases. IEEE Trans. Knowl. Data Eng. 24(1): 86-99 (2012) - [c12]Zayed Albertyn, Jörg Hakenberg
, Hongjin Bian, Huifeng Niu, James Cai:
A high-throughput analysis pipeline for large next generation DNA sequencing studies. BIBM 2012: 1 - 2011
- [j9]Jörg Hakenberg
, Martin Gerner, Maximilian Haeussler, Illés Solt, Conrad Plake, Michael Schroeder, Graciela Gonzalez
, Goran Nenadic
, Casey M. Bergman
:
The GNAT library for local and remote gene mention normalization. Bioinform. 27(19): 2769-2771 (2011) - [j8]Jörg Hakenberg
, Illés Solt, Domonkos Tikk, Nguyen Ha Vo, Luis Tari, Quang Long Nguyen, Chitta Baral, Ulf Leser:
Molecular Event Extraction from Link Grammar Parse Trees in the BioNLP'09 Shared Task. Comput. Intell. 27(4): 665-680 (2011) - 2010
- [j7]Domonkos Tikk, Philippe Thomas, Peter Palaga, Jörg Hakenberg
, Ulf Leser:
A Comprehensive Benchmark of Kernel Methods to Extract Protein-Protein Interactions from Literature. PLoS Comput. Biol. 6(7) (2010) - [j6]Jörg Hakenberg
, Robert Leaman, Nguyen Ha Vo, Siddhartha Jonnalagadda, Ryan Sullivan, Christopher Miller, Luis Tari, Chitta Baral, Graciela Gonzalez
:
Efficient Extraction of Protein-Protein Interactions from Full-Text Articles. IEEE ACM Trans. Comput. Biol. Bioinform. 7(3): 481-494 (2010) - [c11]Syed Toufeeq Ahmed, Radhika Nair, Chintan Patel, Sheela P. Kanwar, Jörg Hakenberg
, Hasan Davulcu:
Semantic classification and dependency parsing enabled automated bio-molecular event extraction from text. BCB 2010: 370-373 - [c10]Luis Tari, Phan Huy Tu, Jörg Hakenberg
, Yi Chen, Tran Cao Son, Graciela Gonzalez
, Chitta Baral:
GenerIE: Information extraction using database queries. ICDE 2010: 1121-1124 - [c9]Luis Tari, Saadat Anwar, Shanshan Liang, Jörg Hakenberg, Chitta Baral:
Synthesis of Pharmacokinetic Pathways through Knowledge Acquisition and Automated Reasoning. Pacific Symposium on Biocomputing 2010: 465-476 - [i3]Siddhartha Jonnalagadda, Luis Tari, Jörg Hakenberg, Chitta Baral, Graciela Gonzalez:
Towards Effective Sentence Simplification for Automatic Processing of Biomedical Text. CoRR abs/1001.4277 (2010)
2000 – 2009
- 2009
- [b1]Jörg Hakenberg:
Mining relations from the biomedical literature. Humboldt University of Berlin, 2009 - [j5]Dimitra Alexopoulou
, Bill Andreopoulos, Heiko Dietze
, Andreas Doms, Fabien Gandon
, Jörg Hakenberg
, Khaled Khelif, Michael Schroeder, Thomas Wächter:
Biomedical word sense disambiguation with ontologies and metadata: automation meets accuracy. BMC Bioinform. 10 (2009) - [j4]Conrad Plake, Loïc Royer
, Rainer Winnenburg
, Jörg Hakenberg
, Michael Schroeder:
GoGene: gene annotation in the fast lane. Nucleic Acids Res. 37(Web-Server-Issue): 300-304 (2009) - [c8]Jörg Hakenberg, Illés Solt, Domonkos Tikk, Luis Tari, Astrid Rheinländer, Quang Long Nguyen, Graciela Gonzalez, Ulf Leser:
Molecular event extraction from Link Grammar parse trees. BioNLP@HLT-NAACL (Shared Task) 2009: 86-94 - [c7]Peter Palaga, Long Nguyen, Ulf Leser, Jörg Hakenberg
:
High-performance information extraction with AliBaba. EDBT 2009: 1140-1143 - [c6]Siddhartha Jonnalagadda, Luis Tari, Jörg Hakenberg, Chitta Baral, Graciela Gonzalez:
Towards Effective Sentence Simplification for Automatic Processing of Biomedical Text. HLT-NAACL (Short Papers) 2009: 177-180 - [c5]Luis Tari, Jörg Hakenberg, Graciela Gonzalez, Chitta Baral:
Querying Parse Tree Database of Medline Text to Synthesize User-Specific Biomolecular Networks. Pacific Symposium on Biocomputing 2009: 87-98 - [p2]Torsten Schiemann, Ulf Leser, Jörg Hakenberg
:
Word Sense Disambiguation in Biomedical Applications. Information Retrieval in Biomedicine 2009: 142-161 - 2008
- [c4]Jörg Hakenberg
, Conrad Plake, Robert Leaman, Michael Schroeder, Graciela Gonzalez
:
Inter-species normalization of gene mentions with GNAT. ECCB 2008: 126-132 - [p1]Thomas Wächter, Dimitra Alexopoulou, Heiko Dietze, Jörg Hakenberg
, Michael Schroeder:
Searching Biomedical Literature with Anatomy Ontologies. Anatomy Ontologies for Bioinformatics 2008: 177-194 - [i2]Heiko Dietze, Dimitra Alexopoulou, Michael R. Alvers, Bill Barrio-Alvers, Andreas Doms, Jörg Hakenberg, Jan Mönnich, Conrad Plake, Andreas Reischuck, Loïc Royer, Thomas Wächter, Matthias Zschunke, Michael Schroeder:
GoPubMed: Exploring Pubmed with Ontological Background Knowledge. Ontologies and Text Mining for Life Sciences 2008 - [i1]Jörg Hakenberg:
Services for annotation of biomedical text. Ontologies and Text Mining for Life Sciences 2008 - 2007
- [c3]Jörg Hakenberg:
What's in a gene name? Automated refinement of gene name dictionaries. BioNLP@ACL 2007: 153-160 - 2006
- [j3]Conrad Plake, Torsten Schiemann, Marcus Pankalla, Jörg Hakenberg
, Ulf Leser:
ALIBABA: PubMed as a graph. Bioinform. 22(19): 2444-2445 (2006) - [c2]Jörg Hakenberg, Ulf Leser, Harald Kirsch, Dietrich Rebholz-Schuhmann:
Collecting a Large Corpus from all of Medline. SMBM 2006 - [e1]Eric G. Bremer, Jörg Hakenberg
, Eui-Hong Han, Daniel P. Berrar, Werner Dubitzky:
Knowledge Discovery in Life Science Literature, PAKDD 2006 International Workshop, KDLL 2006, Singapore, April 9, 2006, Proceedings. Lecture Notes in Computer Science 3886, Springer 2006, ISBN 3-540-32809-2 [contents] - 2005
- [j2]Ulf Leser, Jörg Hakenberg
:
What makes a gene name? Named entity recognition in the biomedical literature. Briefings Bioinform. 6(4): 357-369 (2005) - [j1]Jörg Hakenberg
, Steffen Bickel, Conrad Plake, Ulf Brefeld, Hagen Zahn, Lukas Faulstich, Ulf Leser, Tobias Scheffer:
Systematic feature evaluation for gene name recognition. BMC Bioinform. 6(S-1) (2005) - [c1]Conrad Plake, Jörg Hakenberg
, Ulf Leser:
Optimizing syntax patterns for discovering protein-protein interactions. SAC 2005: 195-201
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